Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~borisevich/term6/Pr13/dimer.top Дата изменения: Wed May 16 17:33:15 2012 Дата индексирования: Tue Oct 2 18:04:44 2012 Кодировка:

;
; File 'dimer.top' was generated
; By user: borisevich (9018)
; On host: kodomo.fbb.msu.ru
; At date: Wed May 2 18:52:45 2012
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.5
;
; Command line was:
; pdb2gmx -f dimer-out.pdb -o dimer -p dimer -ff amber99sb -water tip3p
;
; Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
#include "./amber99sb.ff/forcefield.itp"

[ moleculetype ]
; Name nrexcl
EGL 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 EGL rtp EGL q 0.0
1 CT 1 EGL C1 1 0.0042 12.01 ; qtot 0.0042
2 H1 1 EGL H1 2 0.0553 1.008 ; qtot 0.0595
3 H1 1 EGL H2 3 0.0553 1.008 ; qtot 0.1148
4 H1 1 EGL H3 4 0.0553 1.008 ; qtot 0.1701
5 OS 1 EGL O 5 -0.3632 16 ; qtot -0.1931
6 CT 1 EGL C2 6 0.1385 12.01 ; qtot -0.0546
7 H1 1 EGL H4 7 0.0273 1.008 ; qtot -0.0273
8 H1 1 EGL H5 8 0.0273 1.008 ; qtot 0
; residue 2 EGL rtp EGL q 0.0
9 CT 2 EGL C1 9 0.0042 12.01 ; qtot 0.0042
10 H1 2 EGL H1 10 0.0553 1.008 ; qtot 0.0595
11 H1 2 EGL H2 11 0.0553 1.008 ; qtot 0.1148
12 H1 2 EGL H3 12 0.0553 1.008 ; qtot 0.1701
13 OS 2 EGL O 13 -0.3632 16 ; qtot -0.1931
14 CT 2 EGL C2 14 0.1385 12.01 ; qtot -0.0546
15 H1 2 EGL H4 15 0.0273 1.008 ; qtot -0.0273
16 H1 2 EGL H5 16 0.0273 1.008 ; qtot 0

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
6 7 1
6 8 1
6 14 1
9 10 1
9 11 1
9 12 1
9 13 1
13 14 1
14 15 1
14 16 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 8 1
1 14 1
2 6 1
3 6 1
4 6 1
5 13 1
5 15 1
5 16 1
6 9 1
7 13 1
7 15 1
7 16 1
8 13 1
8 15 1
8 16 1
9 15 1
9 16 1
10 14 1
11 14 1
12 14 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
5 6 7 1
5 6 8 1
5 6 14 1
7 6 8 1
7 6 14 1
8 6 14 1
10 9 11 1
10 9 12 1
10 9 13 1
11 9 12 1
11 9 13 1
12 9 13 1
9 13 14 1
6 14 13 1
6 14 15 1
6 14 16 1
13 14 15 1
13 14 16 1
15 14 16 1

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 9
3 1 5 6 9
4 1 5 6 9
1 5 6 7 9
1 5 6 8 9
1 5 6 14 9
5 6 14 13 9
5 6 14 15 9
5 6 14 16 9
7 6 14 13 9
7 6 14 15 9
7 6 14 16 9
8 6 14 13 9
8 6 14 15 9
8 6 14 16 9
10 9 13 14 9
11 9 13 14 9
12 9 13 14 9
9 13 14 6 9
9 13 14 15 9
9 13 14 16 9

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "./amber99sb.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include "./amber99sb.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
EGL 1
SOL 482